肝细胞癌发生发展关键基因及其功能的生物信息学分析

Bioinformatics analysis of key genes and their functions in occurrence and development hepatocellular carcinoma

背景与目的:肝细胞癌(HCC)是常见的原发性肝癌,其预后较差。基因的激活与失活可促进HCC的发生发展。本研究基于生物信息学HCC发生发展的关键基因及功能并进行临床样本表达验证。方法:从公共基因GEO数据库中筛选HCC及癌旁组织基因芯片,通过GEO2R在线工具及Venn图筛选出差异表达基因(DEGs),对筛选出来的DEGs用DAVID网站进行GO功能分析和KEGG通路富集分析,再用STRING网站及Cytscape软件对DEGs进行蛋白-蛋白相互作用(PPI)网络分析并筛选出核心DEGs,将核心DEGs在Kaplan-Meier Plotter网站进行生存分析,筛选出与预后相关的DEGs,将与预后相关的DEGs用GEPIA网站进行表达量分析,得到在HCC和癌旁组织中的差异表达情况;将与预后相关且在HCC中高表达的DEGs经Metascape网站进行功能及富集通路分析,得到与HCC发生发展有关的关键基因,最后选取关键基因在HCC和癌旁组织标本中进行表达验证。结果:从GEO数据库下载的符合要求的3个基因芯片(GSE14520,GSE41804,GSE45267)中共筛选出78个DEGs。用DAVID网站进行GO功能分析、KEGG通路富集分析、STRING网站及Cytscape软件分析后,筛选出17个核心DEGs(CDK1、ASPM、CENPF、RRM2、CCNB1、TOP2A、PTTG1、ECT2、CDKN3、CYP2B6、SLCO1B3、CYP1A2、CYP4A11、CYP26A1、CYP2E1、NAT2、CYP3A4),将17个核心DEGs在Kaplan-Meier Plotter网站进行生存分析后显示,有9个基因(CDK1、ASPM、CENPF、RRM2、CCNB1、TOP2A、PTTG1、ECT2、CDKN3)与HCC的预后相关(均P<0.05)。GEPIA网站进行表达量分析显示,9个基因在HCC组织中均高表达(均P<0.05)。Metascape网站分析显示,9个高表达基因要富集在细胞有丝分裂的负调控、细胞周期、核染色体隔离和雌配子的产生方面。选取CDK1在HCC组织和癌旁组织中进行验证,结果显示,CDK1在HCC组织中的表达量明显高于癌旁组织(P<0.05)。结论:本研究得到的9个基因可能是HCC发生、发展的关键基因,可为HCC的发生机制的研究以及诊断、治疗提供参考。

Background and Aims:Hepatocellular carcinoma(HCC)is a common primary liver cancer with a poor prognosis.The activation and inactivation of genes can promote the occurrence and development of HCC.This study was conducted to investigate the key genes and their functions in the occurrence and development of HCC based on bioinformatics and verify their expressions in clinical samples.Methods:The HCC and paracancerous tissue gene chips were downloaded from the public gene GEO database,the differentially expressed genes(DEGs)were screened through GEO2R online tools and Venn diagrams,and the GO function analysis and KEGG pathway enrichment analysis were performed on the selected DEGs using the DAVID website,and then the core DEGs were picked up from the DEGs by protein-protein interaction(PPI)network analysis using STRING website and Cytscape software.The prognosis-related DEGs were determined by survival analysis using Kaplan-Meier Plotter website,and the expression levels of the prognosis-related DEGs were analyzed using the GEPIA website to obtain the differential expressions betwen HCC and paracancerous tissue,and then the key genes associated with the occurrence and development of HCC were screened from the highly expressed prognosis-related DEGs in HCC by function and enrichment pathway analysis using Metascape website.Finally,the expression verification of select key genes was performed in the specimens of HCC and paracancerous tissue.Results:A total of 78 DEGs were screened from the three eligible gene chips(GSE14520,GSE41804,GSE45267)downloaded from GEO.Then,17 core DEGs(CDK1,ASPM,CENPF,RRM2,CCNB1,TOP2A,PTTG1,ECT2,CDKN3,CYP2B6,SLCO1B3,CYP1A2,CYP4A11,CYP26A1,CYP2E1,NAT2,CYP3A4)were screened out after using DAVID website GO function analysis and KEGG pathway enrichment analysis as well as STRING website and Cytscape software analysis.After the survival analysis of the 17 core DEGs on Kaplan-Meier Plotter website,9 genes(CDK1,ASPM,CENPF,RRM2,CCNB1,TOP2A,PTTG1,ECT2,CDKN3)were detected to be associated with the prognosis of HCC(all P<0.05).The expression level analysis by GEPIA website showed that all the 9 genes were highly expressed in HCC tissue(all P<0.05).Metascape website analysis showed that the 9 highly expressed genes were mainly enriched in the processes of negative regulation of mitotic cell cycle,nuclear chromosome segregation and female gamete generation.The CDK1 was selected to verify in HCC and paracancerous tissues,and the result showed that the CDK1 expression level was significantly higher than that in paracancerous tissue(P<0.05).Conclusion:The 9 genes obtained in this study may be the key genes in the occurrence and development of HCC,which provide a reference for the study of the pathogenetic mechanism as well as the diagnosis and treatment of HCC.